refactor: deprecate the --rm and --rm-container flags

These flags are not commonly invoked by users, causing issues when cleaning up old containers. Rather than instruct users to use some random flag, just change the default to what is likely to be more common.

tests/unit/app-json.bats

@@ -31,12 +31,12 @@ teardown() {
   assert_success
   assert_output '["/start","web"]'
 
-  run /bin/bash -c "dokku --rm run $TEST_APP ls /app/prebuild.test"
+  run /bin/bash -c "dokku run $TEST_APP ls /app/prebuild.test"
   echo "output: $output"
   echo "status: $status"
   assert_failure
 
-  run /bin/bash -c "dokku --rm run $TEST_APP ls /app/predeploy.test"
+  run /bin/bash -c "dokku run $TEST_APP ls /app/predeploy.test"
   echo "output: $output"
   echo "status: $status"
   assert_success